[sbml-svn] SF.net SVN: sbml:[21152] branches/libsbml-experimental

[<sar...@us...>]

Revision: 21152
          http://sourceforge.net/p/sbml/code/21152
Author:   sarahkeating
Date:     2014-09-23 08:51:23 +0000 (Tue, 23 Sep 2014)
Log Message:
-----------
Merged revision(s) 21137-21151 from trunk/libsbml:

Modified Paths:
--------------
    branches/libsbml-experimental/examples/c++/comp/flattenModelAdvanced.cpp
    branches/libsbml-experimental/src/sbml/Model.cpp
    branches/libsbml-experimental/src/sbml/SBMLDocument.cpp
    branches/libsbml-experimental/src/sbml/SBMLDocument.h
    branches/libsbml-experimental/src/sbml/SBase.cpp
    branches/libsbml-experimental/src/sbml/SBase.h
    branches/libsbml-experimental/src/sbml/annotation/CVTerm.cpp
    branches/libsbml-experimental/src/sbml/annotation/CVTerm.h
    branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms.c
    branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms_newSetters.c
    branches/libsbml-experimental/src/sbml/annotation/test/TestL3ModelHistory.cpp
    branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation.cpp
    branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation2.cpp
    branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationC.c
    branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp
    branches/libsbml-experimental/src/sbml/annotation/test/TestRunner.c
    branches/libsbml-experimental/src/sbml/annotation/test/TestSyncAnnotation.cpp
    branches/libsbml-experimental/src/sbml/annotation/test/TestValidation.cpp
    branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp
    branches/libsbml-experimental/src/sbml/extension/test/TestPackage.h
    branches/libsbml-experimental/src/sbml/extension/test/TestSBMLExtension.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/extension/CompModelPlugin.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/extension/CompSBMLDocumentPlugin.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/extension/test/TestExtensionObjects.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestDeletion.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestExternalModelDefinition.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestModelDefinition.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestPort.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestReadWriteSBase.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestReplacedBy.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestReplacedElement.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestSBaseObjects.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestSBaseRef.c
    branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestSubmodel.c
    branches/libsbml-experimental/src/sbml/packages/comp/util/SBMLResolverRegistry.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/util/SBMLResolverRegistry.h
    branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningConverter.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestURIResolvers.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/validator/CompValidator.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/validator/constraints/CompConsistencyConstraints.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/validator/constraints/ExtModelReferenceCycles.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/validator/constraints/SubmodelReferenceCycles.cpp
    branches/libsbml-experimental/src/sbml/packages/comp/validator/constraints/UnitReplacementCheck.cpp
    branches/libsbml-experimental/src/sbml/xml/XMLOutputStream.cpp
    branches/libsbml-experimental/src/sbml/xml/test/TestCopyAndClone.cpp
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLAttributes.cpp
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLAttributesC.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLErrorLog.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLInputStream.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLNamespaces.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLNode.cpp
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLNode_newSetters.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLOutputStream.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLToken.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLToken_newSetters.c
    branches/libsbml-experimental/src/sbml/xml/test/TestXMLTriple.c

Property Changed:
----------------
    branches/libsbml-experimental/
    branches/libsbml-experimental/examples/c++/

Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental	2014-09-23 08:51:23 UTC (rev 21152)

Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -2,4 +2,4 ##
 /branches/libsbml-4:9056-10118
 /branches/libsbml-5-conversion:14155-14227
 /branches/libsbml-ast-plugin:16251-19654
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-21136
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-21151
\ No newline at end of property
Index: branches/libsbml-experimental/examples/c++
===================================================================
--- branches/libsbml-experimental/examples/c++	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/examples/c++	2014-09-23 08:51:23 UTC (rev 21152)

Property changes on: branches/libsbml-experimental/examples/c++
___________________________________________________________________
Modified: svn:mergeinfo
## -1,3 +1,3 ##
 /branches/L3Parser/examples/c++:15528-15625,15656-15673
 /branches/libsbml-5-conversion/examples/c++:14155-14227
-/trunk/libsbml/examples/c++:2142-12017,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18294-18310,18312-18353,18390-18443,18450-18454,18456-18458,18586-18638,18644-18715,18921-18944,18976-19112,19193-19195,19538-19551,19709-19749,19765-19793,19797-19821,19851-19866,19881-19905,19927-19949
+/trunk/libsbml/examples/c++:2142-12017,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18294-18310,18312-18353,18390-18443,18450-18454,18456-18458,18586-18638,18644-18715,18921-18944,18976-19112,19193-19195,19538-19551,19709-19749,19765-19793,19797-19821,19851-19866,19881-19905,19927-19949,21137-21151
\ No newline at end of property
Modified: branches/libsbml-experimental/examples/c++/comp/flattenModelAdvanced.cpp
===================================================================
--- branches/libsbml-experimental/examples/c++/comp/flattenModelAdvanced.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/examples/c++/comp/flattenModelAdvanced.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -67,155 +67,151 @@
 class CPrefixNameTransformer : public PrefixTransformer
 {
 public:
-	CPrefixNameTransformer() {}
+  CPrefixNameTransformer() {}
 
-	static void replaceStringInPlace(std::string& subject, const std::string& search,
-	const std::string& replace)
-	{
-		size_t pos = 0;
+  static void replaceStringInPlace(std::string& subject, const std::string& search,
+  const std::string& replace)
+  {
+    size_t pos = 0;
 
-		while ((pos = subject.find(search, pos)) != std::string::npos)
-		{
-			subject.replace(pos, search.length(), replace);
-			pos += replace.length();
-		}
-	}
+    while ((pos = subject.find(search, pos)) != std::string::npos)
+    {
+      subject.replace(pos, search.length(), replace);
+      pos += replace.length();
+    }
+  }
 
-	static inline std::string &rtrim(std::string &str)
-	{
-		size_t endpos = str.find_last_not_of(" \t");
+  static inline std::string &rtrim(std::string &str)
+  {
+    size_t endpos = str.find_last_not_of(" \t");
 
-		if (string::npos != endpos)
-		{
-			str = str.substr(0, endpos + 1);
-		}
+    if (string::npos != endpos)
+    {
+      str = str.substr(0, endpos + 1);
+    }
 
-		return str;
-	}
+    return str;
+  }
 
-	const std::string& cleanName(std::string& prefix)
-	{
-		std::replace(prefix.begin(), prefix.end(), '_', ' ');
-		replaceStringInPlace(prefix, "  ", " ");
-		rtrim(prefix);
-		return prefix;
-	}
+  const std::string& cleanName(std::string& prefix)
+  {
+    std::replace(prefix.begin(), prefix.end(), '_', ' ');
+    replaceStringInPlace(prefix, "  ", " ");
+    rtrim(prefix);
+    return prefix;
+  }
 
-	virtual int transform(SBase* element)
-	{
-		if (element == NULL || getPrefix().empty())
-		return LIBSBML_OPERATION_SUCCESS;
+  virtual int transform(SBase* element)
+  {
+    if (element == NULL || getPrefix().empty())
+    return LIBSBML_OPERATION_SUCCESS;
 
-		// set up ids
+    // set up ids
     // this will rename the SIds and SIdRefs as
     // the comp flattening routine does by default
-		PrefixTransformer::transform(element);
+    PrefixTransformer::transform(element);
 
-		// skip local parameters, as they are not renamed
-		if (element->getTypeCode() == SBML_LOCAL_PARAMETER)
-		return LIBSBML_OPERATION_SUCCESS;
+    // skip local parameters, as they are not renamed
+    if (element->getTypeCode() == SBML_LOCAL_PARAMETER)
+    return LIBSBML_OPERATION_SUCCESS;
 
-		// setup names
+    // setup names
     // here we want to rename the name attribute to also indicate if
     // the element came from a subModel
-		if (element->isSetName())
-		{
-			std::stringstream newName;
-			std::string prefix = getPrefix();
-			newName << element->getName() << " (" << cleanName(prefix) << ")";
-			element->setName(newName.str());
-		}
+    if (element->isSetName())
+    {
+      std::stringstream newName;
+      std::string prefix = getPrefix();
+      newName << element->getName() << " (" << cleanName(prefix) << ")";
+      element->setName(newName.str());
+    }
 
-		return LIBSBML_OPERATION_SUCCESS;
-	}
+    return LIBSBML_OPERATION_SUCCESS;
+  }
 };
 
 
 int main(int argc,char** argv)
 {
-	bool leavePorts = false;
-	if (argc < 3)
-	{
-		cout << usage << endl;
-		return 1;
-	}
-	else if (argc == 3)
-	{
-		if ( string("-p") == string(argv[1]) )
-		{
-			cout << usage << endl;
-			return 1;
-		}       
-	}
+  bool leavePorts = false;
+  if (argc < 3)
+  {
+    cout << usage << endl;
+    return 1;
+  }
+  else if (argc == 3)
+  {
+    if ( string("-p") == string(argv[1]) )
+    {
+      cout << usage << endl;
+      return 1;
+    }       
+  }
 
-	int  argIndex = 1;
+  int  argIndex = 1;
 
-	if ( string("-p") == string(argv[1]) )
-	{
-		leavePorts = true;
-		++argIndex;
-	}     
+  if ( string("-p") == string(argv[1]) )
+  {
+    leavePorts = true;
+    ++argIndex;
+  }     
 
-	if (SBMLExtensionRegistry::isPackageEnabled("comp") == false)
-	{
-		cerr << "The version of libsbml being used does not have the comp"
-		     << " package code enabled" << endl;
-		return 1;
-	}
+  if (SBMLExtensionRegistry::isPackageEnabled("comp") == false)
+  {
+    cerr << "The version of libsbml being used does not have the comp"
+         << " package code enabled" << endl;
+    return 1;
+  }
 
-	const char* inputFile   = argv[argIndex];
-	const char* outputFile  = argv[argIndex+1];
+  const char* inputFile   = argv[argIndex];
+  const char* outputFile  = argv[argIndex+1];
 
-	SBMLDocument* document = readSBML(inputFile);
+  SBMLDocument* document = readSBML(inputFile);
 
-	if (document->getNumErrors() > 0)
-	{
-		cerr << "Encountered the following SBML errors:" << endl;
-		document->printErrors(cerr);
-		return 1;
-	}
+  if (document->getNumErrors() > 0)
+  {
+    cerr << "Encountered the following SBML errors:" << endl;
+    document->printErrors(cerr);
+    return 1;
+  }
 
-	// add the advanced prefix transformer to the comp plugin
+  // add the advanced prefix transformer to the comp plugin
   // this transformer will be used during the flattening process
   // to rename SIds and SIdRefs (as would happen by default)
   // but allows the user to specify other changes that they
-  // may wsh to be made (e.g. rename the name attribute)
-	CompModelPlugin* mPlug = dynamic_cast<CompModelPlugin*>(document->getModel()->getPlugin("comp"));
-	CPrefixNameTransformer trans;
+  // may wish to be made (e.g. rename the name attribute)
+  CompModelPlugin* mPlug = dynamic_cast<CompModelPlugin*>(document->getModel()->getPlugin("comp"));
+  CPrefixNameTransformer trans;
 
-	if (mPlug != NULL)
-	{
-		mPlug->setTransformer(&trans);
-	}
+  if (mPlug != NULL)
+  {
+    mPlug->setTransformer(&trans);
+  }
 
-	ConversionProperties* props = new ConversionProperties();
+  ConversionProperties* props = new ConversionProperties();
 
-	props->addOption("flatten comp");
-	props->addOption("leavePorts", leavePorts);
+  props->addOption("flatten comp");
+  props->addOption("leavePorts", leavePorts);
 
-	SBMLConverter* converter = 
-	SBMLConverterRegistry::getInstance().getConverterFor(*props);
+  SBMLConverter* converter = 
+  SBMLConverterRegistry::getInstance().getConverterFor(*props);
 
 
-	converter->setDocument(document);
+  converter->setDocument(document);
 
-	int result = converter->convert();
+  // NOTE: after a call to convert, the comp model plugin pointer 
+  // is no longer valid and has to be retrieved again. 
+  int result = converter->convert();
 
-	if (result != LIBSBML_OPERATION_SUCCESS)
-	{
-		cerr << "Conversion failed\n";
-		document->printErrors();
-	}
+  if (result != LIBSBML_OPERATION_SUCCESS)
+  {
+    cerr << "Conversion failed\n";
+    document->printErrors();
+  }
+  
+  writeSBML(document, outputFile);
 
-	// unset the transformer before it goes out of scope
-	if (mPlug != NULL)
-	{
-		mPlug->setTransformer(NULL);
-	}
+  delete converter;
+  delete document;
 
-	writeSBML(document, outputFile);
-
-	delete converter;
-	delete document;
-
 }

Modified: branches/libsbml-experimental/src/sbml/Model.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/Model.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/Model.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -4778,7 +4778,7 @@
       Unit* uFromModel = getUnitDefinition("substance")->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -4823,7 +4823,7 @@
       Unit* uFromModel = getUnitDefinition(substanceUnits)->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -4881,7 +4881,7 @@
       Unit* uFromModel = getUnitDefinition("time")->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -4926,7 +4926,7 @@
       Unit* uFromModel = getUnitDefinition(timeUnits)->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -4984,7 +4984,7 @@
       Unit* uFromModel = getUnitDefinition("volume")->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -5029,7 +5029,7 @@
       Unit* uFromModel = getUnitDefinition(volumeUnits)->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -5087,7 +5087,7 @@
       Unit* uFromModel = getUnitDefinition("area")->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -5133,7 +5133,7 @@
       Unit* uFromModel = getUnitDefinition(areaUnits)->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -5191,7 +5191,7 @@
       Unit* uFromModel = getUnitDefinition("length")->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }
@@ -5236,7 +5236,7 @@
       Unit* uFromModel = getUnitDefinition(lengthUnits)->getUnit(n);
       if (uFromModel  != NULL)
       {
-        ud->addUnit(uFromModel->clone());
+        ud->addUnit(uFromModel);
       }
     }
   }

Modified: branches/libsbml-experimental/src/sbml/SBMLDocument.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/SBMLDocument.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/SBMLDocument.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -353,6 +353,13 @@
 }
 
 
+bool 
+SBMLDocument::isSetModel() const
+{
+  return mModel != NULL;
+}
+
+
 /*
  * @return the Model contained in this SBMLDocument.
  */
@@ -1939,6 +1946,14 @@
 
 
 LIBSBML_EXTERN
+int
+SBMLDocument_isSetModel(const SBMLDocument_t *d)
+{
+  return (d != NULL) ? (int)d->isSetModel() : 0;
+}
+
+
+LIBSBML_EXTERN
 Model_t *
 SBMLDocument_getModel (SBMLDocument_t *d)
 {

Modified: branches/libsbml-experimental/src/sbml/SBMLDocument.h
===================================================================
--- branches/libsbml-experimental/src/sbml/SBMLDocument.h	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/SBMLDocument.h	2014-09-23 08:51:23 UTC (rev 21152)
@@ -464,7 +464,16 @@
   virtual SBMLDocument* clone () const;
 
 
+
   /**
+  * Returns @c true if the Model object has been set, otherwise 
+  * returns @c false.
+  *
+  * @return @c true if the Model object has been set
+  */
+  bool isSetModel () const;
+
+  /**
    * Returns the Model object stored in this SBMLDocument.
    *
    * It is important to note that this method <em>does not create</em> a
@@ -1728,6 +1737,22 @@
 
 
 /**
+ * Predicate for testing whether the identifier of a given SBMLDocument_t
+ * structure is assigned.
+ *
+ * @param d the SBMLDocument_t structure
+ *
+ * @return nonzero if the model object of this SBMLDocument_t structure is
+ * set, zero (0) otherwise.
+ *
+ * @memberof SBMLDocument_t
+ */
+LIBSBML_EXTERN
+int
+SBMLDocument_isSetModel(const SBMLDocument_t *d);
+
+
+/**
  * Returns the Model_t structure stored in this SBMLDocument_t structure.
  *
  * @param d the SBMLDocument_t structure

Modified: branches/libsbml-experimental/src/sbml/SBase.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/SBase.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/SBase.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -86,7 +86,7 @@
 struct ClonePluginEntity : public unary_function<SBasePlugin*, SBasePlugin*>
 {
   SBasePlugin* operator() (SBasePlugin* sb) {
-    if (!sb) return 0;
+    if (!sb) return NULL;
     return sb->clone();
   }
 };
@@ -281,8 +281,9 @@
  * Creates a new SBase object with the given level and version.
  * Only subclasses may create SBase objects.
  */
-SBase::SBase (unsigned int level, unsigned int version) :
-   mNotes     ( NULL )
+SBase::SBase (unsigned int level, unsigned int version) 
+ : mMetaId ("")
+ , mNotes(NULL)
  , mAnnotation( NULL )
  , mSBML      ( NULL )
  , mSBMLNamespaces (NULL)
@@ -324,8 +325,9 @@
  * Creates a new SBase object with the given SBMLNamespaces.
  * Only subclasses may create SBase objects.
  */
-SBase::SBase (SBMLNamespaces *sbmlns) :
-   mNotes     ( NULL )
+SBase::SBase (SBMLNamespaces *sbmlns) 
+ : mMetaId("")
+ , mNotes(NULL)
  , mAnnotation( NULL )
  , mSBML      ( NULL )
  , mSBMLNamespaces (NULL)
@@ -482,6 +484,7 @@
   mHasBeenDeleted = true;
 
   for_each( mPlugins.begin(), mPlugins.end(), DeletePluginEntity() );
+  deleteDisabledPlugins(false);
 }
 
 /*
@@ -1473,7 +1476,9 @@
     }
     else
     {
-      success = setAnnotation(mAnnotation->clone());
+      XMLNode *copy = mAnnotation->clone();
+      success = setAnnotation(copy);
+      delete copy;
     }
 
 
@@ -1652,9 +1657,10 @@
   if(annt_xmln != NULL)
   {
     success = replaceTopLevelAnnotationElement(annt_xmln);
-    delete annt_xmln;
   }
 
+  delete annt_xmln;
+
   return success;
 }
 
@@ -3041,6 +3047,27 @@
   return (int)mPlugins.size();
 }
 
+unsigned int
+SBase::getNumDisabledPlugins() const
+{
+  return (int)mDisabledPlugins.size();
+}
+
+void 
+SBase::deleteDisabledPlugins(bool recursive /*= true*/)
+{
+  for_each(mDisabledPlugins.begin(), mDisabledPlugins.end(), DeletePluginEntity());
+  mDisabledPlugins.clear();
+
+  if (recursive)
+  {
+    List* list = getAllElements();
+    for (unsigned int i = 0; i < list->getSize(); ++i)
+      ((SBase*)list->get(i))->deleteDisabledPlugins();
+  }
+
+}
+
 int
 SBase::disablePackage(const std::string& pkgURI, const std::string& prefix)
 {
@@ -3163,27 +3190,51 @@
     {
 #if 0
       cout << "[DEBUG] SBase::enablePackageInternal() (uri) " <<  pkgURI
-           << " (prefix) " << pkgPrefix << " (element) " << getElementName() << endl;
+        << " (prefix) " << pkgPrefix << " (element) " << getElementName() << endl;
 #endif
-      mSBMLNamespaces->addNamespace(pkgURI,pkgPrefix);
+      mSBMLNamespaces->addNamespace(pkgURI, pkgPrefix);
     }
 
     //
-    // enable the given package
+    // go through disabled plugins, and if we have one re-enable that one, rather 
+    // than creating a new one
     //
-    const SBMLExtension* sbmlext = SBMLExtensionRegistry::getInstance().getExtensionInternal(pkgURI);
 
-    if (sbmlext)
+    bool wasDisabled = false;
+    int numDisabledPlugins = (int)mDisabledPlugins.size();
+    for (int i = numDisabledPlugins - 1; i >= 0; --i)
     {
-      SBaseExtensionPoint extPoint(getPackageName(),getTypeCode());
-      const SBasePluginCreatorBase* sbPluginCreator = sbmlext->getSBasePluginCreator(extPoint);
-      if (sbPluginCreator)
+      SBasePlugin *current = mDisabledPlugins[i];
+      std::string uri = current->getURI();
+      if (pkgURI == uri)
       {
-        SBasePlugin* entity = sbPluginCreator->createPlugin(pkgURI,pkgPrefix,getNamespaces());
-        entity->connectToParent(this);
-        mPlugins.push_back(entity);
+        mDisabledPlugins.erase(mDisabledPlugins.begin() + i);
+        current->connectToParent(this);
+        mPlugins.push_back(current);
+        wasDisabled = true;
       }
+    }
 
+
+    if (!wasDisabled)
+    {
+      //
+      // enable the given package
+      //
+      const SBMLExtension* sbmlext = SBMLExtensionRegistry::getInstance().getExtensionInternal(pkgURI);
+
+      if (sbmlext)
+      {
+        SBaseExtensionPoint extPoint(getPackageName(), getTypeCode());
+        const SBasePluginCreatorBase* sbPluginCreator = sbmlext->getSBasePluginCreator(extPoint);
+        if (sbPluginCreator)
+        {
+          SBasePlugin* entity = sbPluginCreator->createPlugin(pkgURI, pkgPrefix, getNamespaces());
+          entity->connectToParent(this);
+          mPlugins.push_back(entity);
+        }
+      }
+
     }
     /* check whether we are trying to reenable an unknown package
      * that we previously disabled
@@ -3221,12 +3272,15 @@
     //
     // disable the given package
     //
-    for (size_t i=0; i < mPlugins.size(); i++)
+    int numPlugins = (int)mPlugins.size();
+    for (int i=numPlugins-1; i >= 0; --i)
     {
-      std::string uri = mPlugins[i]->getURI();
+      SBasePlugin *current = mPlugins[i];
+      std::string uri = current->getURI();
       if (pkgURI == uri)
-      {
+      {        
         mPlugins.erase( mPlugins.begin() + i );
+        mDisabledPlugins.push_back(current);
       }
     }
 

Modified: branches/libsbml-experimental/src/sbml/SBase.h
===================================================================
--- branches/libsbml-experimental/src/sbml/SBase.h	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/SBase.h	2014-09-23 08:51:23 UTC (rev 21152)
@@ -2672,6 +2672,28 @@
 
 
   /**
+   * Returns the number of disabled plug-in objects (extenstion interfaces) 
+   * for SBML Level&nbsp;3 package extensions known.
+   *
+   * @copydetails doc_what_are_plugins
+   *
+   * @return the number of disabled plug-in objects (extension interfaces) 
+   * of package extensions known by this instance of libSBML.
+   *
+   */
+  unsigned int getNumDisabledPlugins() const;
+
+  /** 
+   * Deletes all information stored in disabled plugins. 
+   *
+   * @param recursive if @c true, the disabled information will be deleted
+   * also from all child elements, otherwise only from this SBase element.
+   *
+   * @see getNumDisabledPlugins()
+   */
+  void deleteDisabledPlugins(bool recursive=true);
+
+  /**
    * Enables or disables the given SBML Level&nbsp;3 package on this object.
    *
    * This method enables the specified package on this object and other
@@ -3644,7 +3666,13 @@
   //
   std::vector<SBasePlugin*> mPlugins;
 
+  //
+  // In case an SBasePlugin is disabled, we still store it here in case it 
+  // will be re-enabled later on. 
+  //
+  std::vector<SBasePlugin*> mDisabledPlugins;
 
+
   //
   // namespace to which this SBase object belongs.
   // This variable can be publicly accessible by getElementNamespace function.

Modified: branches/libsbml-experimental/src/sbml/annotation/CVTerm.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/CVTerm.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/CVTerm.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -287,6 +287,13 @@
 }
 
 
+QualifierType_t 
+CVTerm::getQualifierType() const
+{
+  return mQualifier;
+}
+
+
 /*
  * gets the Model Qualifier type
  */
@@ -297,6 +304,13 @@
 }
 
 
+ModelQualifierType_t 
+CVTerm::getModelQualifierType() const
+{
+  return mModelQualifier;
+}
+
+
 /*
  * gets the biological Qualifier type
  */
@@ -307,6 +321,13 @@
 }
 
 
+BiolQualifierType_t 
+CVTerm::getBiologicalQualifierType() const
+{
+  return mBiolQualifier;
+}
+
+
 /*
  * gets the resources
  */
@@ -336,6 +357,13 @@
 }
 
   
+unsigned int 
+CVTerm::getNumResources() const
+{
+  return mResources->getLength();
+}
+
+  
 /*
  * Returns the value of the nth resource for this %CVTerm.
  */
@@ -347,6 +375,16 @@
 
   
 /*
+ * Returns the value of the nth resource for this %CVTerm.
+ */
+std::string
+CVTerm::getResourceURI(unsigned int n) const
+{
+  return mResources->getValue(n);
+}
+
+  
+/*
  * adds a resource to the term
  */
 int 
@@ -433,6 +471,41 @@
   return valid;
 }
 
+bool 
+CVTerm::hasRequiredAttributes() const
+{
+  bool valid = true;
+
+  if (getQualifierType() == UNKNOWN_QUALIFIER)
+  {
+    valid = false;
+  }
+  else if (getQualifierType() == MODEL_QUALIFIER)
+  {
+    if (getModelQualifierType() == BQM_UNKNOWN)
+    {
+      valid = false;
+    }
+  }
+  else
+  {
+    if (getBiologicalQualifierType() == BQB_UNKNOWN)
+    {
+      valid = false;
+    }
+  }
+
+  if (valid)
+  {
+    if (getResources()->isEmpty())
+    {
+      valid = false;
+    }
+  }
+
+  return valid;
+}
+
 bool
 CVTerm::hasBeenModified()
 {

Modified: branches/libsbml-experimental/src/sbml/annotation/CVTerm.h
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/CVTerm.h	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/CVTerm.h	2014-09-23 08:51:23 UTC (rev 21152)
@@ -525,7 +525,12 @@
    */
   QualifierType_t getQualifierType();
 
+  /** @cond doxygenLibsbmlInternal */
 
+  QualifierType_t getQualifierType() const;
+
+  /** @endcond */
+
   /**
    * Returns the model qualifier type of this CVTerm object.
    * 
@@ -567,6 +572,12 @@
   ModelQualifierType_t getModelQualifierType();
 
 
+  /** @cond doxygenLibsbmlInternal */
+
+  ModelQualifierType_t getModelQualifierType() const;
+
+  /** @endcond */
+
   /**
    * Returns the biological qualifier type of this CVTerm object.
    * 
@@ -617,6 +628,12 @@
   BiolQualifierType_t getBiologicalQualifierType();
 
 
+  /** @cond doxygenLibsbmlInternal */
+
+  BiolQualifierType_t getBiologicalQualifierType() const;
+
+  /** @endcond */
+
   /**
    * Returns the resource references for this CVTerm object.
    *
@@ -687,6 +704,27 @@
    */
   unsigned int getNumResources(); 
 
+
+  /**
+   * Returns the number of resources for this CVTerm object.
+   * 
+   * @copydetails doc_cvterm_common_description
+   *
+   * The fragment above illustrates that there can be more than one
+   * resource referenced by a given relationship annotation (i.e., the
+   * <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> values associated with a particular <span class="code"
+   * style="background-color: #bbb">RELATION_ELEMENT</span>).  The present
+   * method returns a count of the resources stored in this CVTerm object.
+   *
+   * @return the number of resources in the set of XMLAttributes
+   * of this CVTerm.
+   *
+   * @see getResources()
+   * @see getResourceURI(unsigned int n)
+   */
+  unsigned int getNumResources() const;
+
   
   /**
    * Returns the value of the <em>n</em>th resource for this CVTerm object.
@@ -715,6 +753,32 @@
 
   
   /**
+   * Returns the value of the <em>n</em>th resource for this CVTerm object.
+   *
+   * @copydetails doc_cvterm_common_description
+   *
+   * The fragment above illustrates that there can be more than one
+   * resource referenced by a given relationship annotation (i.e., the
+   * <span class="code" style="background-color: #d0d0ee">resource
+   * URI</span> values associated with a particular <span class="code"
+   * style="background-color: #bbb">RELATION_ELEMENT</span>).  LibSBML
+   * stores all resource URIs in a single CVTerm object for a given
+   * relationship.  Callers can use getNumResources() to find out how many
+   * resources are stored in this CVTerm object, then call this method to
+   * retrieve the <em>n</em>th resource URI.
+   * 
+   * @param n the index of the resource to query
+   *
+   * @return string representing the value of the nth resource
+   * in the set of XMLAttributes of this CVTerm.
+   *
+   * @see getNumResources()
+   * @see getQualifierType()
+   */
+  std::string getResourceURI(unsigned int n) const; 
+  
+  
+  /**
    * Sets the @if clike #QualifierType_t@else qualifier code@endif@~ of this
    * CVTerm object.
    *
@@ -923,6 +987,7 @@
 
   void resetModifiedFlags();
    
+  bool hasRequiredAttributes() const;
   
   /** @endcond */
 

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms.c
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms.c	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms.c	2014-09-23 08:51:23 UTC (rev 21152)
@@ -118,7 +118,6 @@
   XMLNode_addChild(bag, li);
   XMLNode_addChild(node, bag);
 
-
   CVTerm_t *term = CVTerm_createFromNode(node);
 
   fail_unless(term != NULL);
@@ -128,9 +127,16 @@
   xa = CVTerm_getResources(term);
 
   fail_unless(XMLAttributes_getLength(xa) == 1);
-  fail_unless(!strcmp(XMLAttributes_getName(xa, 0), "rdf:resource"));
-  fail_unless(!strcmp(XMLAttributes_getValue(xa, 0), "This is my resource"));
+  
+  char * name = XMLAttributes_getName(xa, 0);
+  char * value = XMLAttributes_getValue(xa, 0);
+  
+  fail_unless(!strcmp(name, "rdf:resource"));
+  fail_unless(!strcmp(value, "This is my resource"));
 
+  free(name);
+  free(value);
+
   XMLTriple_free(qual_triple);
   XMLTriple_free(bag_triple);
   XMLTriple_free(li_triple);
@@ -143,8 +149,6 @@
   XMLNode_free(node);
   XMLNode_free(bag);
   XMLNode_free(li);
-  
-
 }
 END_TEST
 
@@ -162,13 +166,17 @@
   xa = CVTerm_getResources(term);
 
   fail_unless(XMLAttributes_getLength(xa) == 1);
-  fail_unless(!strcmp(XMLAttributes_getName(xa, 0), "rdf:resource"));
-  fail_unless(!strcmp(XMLAttributes_getValue(xa, 0), "GO6666"));
 
+  char * name = XMLAttributes_getName(xa, 0);
+  char * value = XMLAttributes_getValue(xa, 0);
+  
+  fail_unless(!strcmp(name, "rdf:resource"));
+  fail_unless(!strcmp(value, "GO6666"));
 
+  free(name);
+  free(value);
   
   CVTerm_free(term);
-
 }
 END_TEST
 
@@ -186,13 +194,17 @@
   number = CVTerm_getNumResources(term);
 
   fail_unless(number == 2);
-  fail_unless(!strcmp(CVTerm_getResourceURI(term, 0), "GO6666"));
-  fail_unless(!strcmp(CVTerm_getResourceURI(term, 1), "OtherURI"));
 
+  char * res1 = CVTerm_getResourceURI(term, 0);
+  char * res2 = CVTerm_getResourceURI(term, 1);
 
+  fail_unless(!strcmp(res1, "GO6666"));
+  fail_unless(!strcmp(res2, "OtherURI"));
+
+  free(res1);
+  free(res2);
   
   CVTerm_free(term);
-
 }
 END_TEST
 
@@ -221,13 +233,11 @@
 	
   fail_unless (ModelQualifierType_fromString(NULL) == BQM_UNKNOWN);
 	fail_unless (BiolQualifierType_fromString(NULL) == BQB_UNKNOWN);
-
 }
 END_TEST
 
 START_TEST (test_CVTerm_get_biol_qualifiers)
 {
-  
   fail_unless (BiolQualifierType_fromString("is") == BQB_IS);
   fail_unless (BiolQualifierType_fromString("hasPart") == BQB_HAS_PART);
   fail_unless (BiolQualifierType_fromString("isPartOf") == BQB_IS_PART_OF);
@@ -256,7 +266,6 @@
   fail_unless (strcmp(BiolQualifierType_toString(BQB_HAS_PROPERTY), "hasProperty") == 0);
   fail_unless (strcmp(BiolQualifierType_toString(BQB_IS_PROPERTY_OF), "isPropertyOf") == 0);
   fail_unless (BiolQualifierType_toString(BQB_UNKNOWN) ==  NULL); 
-
 }
 END_TEST
 

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms_newSetters.c
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms_newSetters.c	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestCVTerms_newSetters.c	2014-09-23 08:51:23 UTC (rev 21152)
@@ -137,9 +137,16 @@
   xa = CVTerm_getResources(term);
 
   fail_unless(XMLAttributes_getLength(xa) == 1);
-  fail_unless(!strcmp(XMLAttributes_getName(xa, 0), "rdf:resource"));
-  fail_unless(!strcmp(XMLAttributes_getValue(xa, 0), "GO6666"));
+  
+  char * name = XMLAttributes_getName(xa, 0);
+  char * value = XMLAttributes_getValue(xa, 0);
+  
+  fail_unless(!strcmp(name, "rdf:resource"));
+  fail_unless(!strcmp(value, "GO6666"));
 
+  free(name);
+  free(value);
+
   CVTerm_free(term);
 }
 END_TEST

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestL3ModelHistory.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestL3ModelHistory.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestL3ModelHistory.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -69,6 +69,8 @@
   d = readSBML(filename);
   m = d->getModel();
   c = m->getCompartment(0);
+
+  delete filename;
 }
 
 
@@ -255,6 +257,7 @@
   fail_unless( equals(expected, n1->toXMLString().c_str()) );
 
   delete node;
+  delete n1;
 }
 END_TEST
 
@@ -418,9 +421,11 @@
     "  </annotation>\n"
     "</compartment>";
 
+  char * sbml = c->toSBML();
 
-  fail_unless( equals(expected, c->toSBML()) );
+  fail_unless( equals(expected, sbml) );
 
+  delete sbml;
 }
 END_TEST
 
@@ -657,18 +662,22 @@
                             L3ModelHistory_setup,
                             L3ModelHistory_teardown);
 
+  // libxml leaks these but expat does not
   tcase_add_test(tcase, test_L3ModelHistory_getModelHistory );
   tcase_add_test(tcase, test_L3ModelHistory_parseModelHistory );
-  tcase_add_test(tcase, test_L3ModelHistory_delete );
-  tcase_add_test(tcase, test_L3ModelHistory_deleteWithOther );
-//  tcase_add_test(tcase, test_L3ModelHistory_recreate );
-//  tcase_add_test(tcase, test_L3ModelHistory_recreateFromEmpty );
   tcase_add_test(tcase, test_L3ModelHistory_deleteWithOutOther );
   tcase_add_test(tcase, test_L3ModelHistory_recreateWithOutOther );
   tcase_add_test(tcase, test_L3ModelHistory_getModelHistory_Model );
   tcase_add_test(tcase, test_L3ModelHistory_parseModelHistory_Model );
+
+  // // memory leaks unresolved
+  // leaks XMLNodes removeChild
+  tcase_add_test(tcase, test_L3ModelHistory_delete );
+  tcase_add_test(tcase, test_L3ModelHistory_deleteWithOther );
   tcase_add_test(tcase, test_L3ModelHistory_delete_Model );
-//  tcase_add_test(tcase, test_L3ModelHistory_recreateFromEmpty_Model );
+
+  
+  
   suite_add_tcase(suite, tcase);
 
   return suite;

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -69,6 +69,8 @@
   // The following will return a pointer to a new SBMLDocument.
   d = readSBML(filename);
   m = d->getModel();
+
+  free(filename);
 }
 
 
@@ -519,11 +521,12 @@
   
   // unset metaid ... now we have potentially dangling RDF
   model->setMetaId("");
-  std::string test = model->toSBML();
+  char * test = model->toSBML();
 
   // this should be the test
-  fail_unless(test == "<model id=\"test1\"/>");   
+  fail_unless(!strcmp(test, "<model id=\"test1\"/>"));
 
+  free(test);
 }
 END_TEST
 
@@ -633,11 +636,13 @@
   
   // unset metaid ... now we have potentially dangling RDF
   model->setMetaId("");
-  std::string test = model->toSBML();
+  char * test = model->toSBML();
 
   // this should be the test
-  fail_unless(test == "<model id=\"test1\"/>");   
+  fail_unless(!strcmp(test, "<model id=\"test1\"/>"));  
 
+  free(test);
+
 }
 END_TEST
 
@@ -2060,16 +2065,9 @@
   tcase_add_test(tcase, test_invalid_user_annotation );
   tcase_add_test(tcase, test_RDFAnnotation_getModelHistory );
   tcase_add_test(tcase, test_RDFAnnotation_parseModelHistory );
-  tcase_add_test(tcase, test_RDFAnnotation_parseCVTerms );
-  tcase_add_test(tcase, test_RDFAnnotation_delete );
-  tcase_add_test(tcase, test_RDFAnnotation_deleteWithOther );
-//  tcase_add_test(tcase, test_RDFAnnotation_recreate );
-//  tcase_add_test(tcase, test_RDFAnnotation_recreateFromEmpty );
   tcase_add_test(tcase, test_RDFAnnotation_deleteWithOutOther );
   tcase_add_test(tcase, test_RDFAnnotation_deleteWithOtherRDF );
-//  tcase_add_test(tcase, test_RDFAnnotation_recreateWithOutOther );
   tcase_add_test(tcase, test_RDFAnnotation_testMissingMetaId );
-  tcase_add_test(tcase, test_RDFAnnotation_testMissingAbout );
   tcase_add_test(tcase, test_RDFAnnotation_testAnnotationForMetaId );
   tcase_add_test(tcase, test_RDFAnnotation_testHasRDFAnnotation );
   tcase_add_test(tcase, test_RDFAnnotation_testHasAdditionalRDFAnnotation );
@@ -2078,13 +2076,21 @@
   tcase_add_test(tcase, test_RDFAnnotation_testHasCVTermRDFAnnotationBadAbout );
   tcase_add_test(tcase, test_RDFAnnotation_testHasHistoryRDFAnnotationBadAbout );
   tcase_add_test(tcase, test_RDFAnnotation_testCreateAnnotations );
-  tcase_add_test(tcase, test_RDFAnnotation_deleteCVTerms );
   tcase_add_test(tcase, test_RDFAnnotation_removeSingleAnnotation );
   tcase_add_test(tcase, test_RDFAnnotation_removeSingleAnnotation1 );
   tcase_add_test(tcase, test_RDFAnnotation_removeAnnotation );
+  
+  // // memory leaks unresolved
+  tcase_add_test(tcase, test_RDFAnnotation_parseCVTerms );
+  tcase_add_test(tcase, test_RDFAnnotation_delete );
+  tcase_add_test(tcase, test_RDFAnnotation_deleteWithOther );
+  tcase_add_test(tcase, test_RDFAnnotation_testMissingAbout );
+  tcase_add_test(tcase, test_RDFAnnotation_deleteCVTerms );
   tcase_add_test(tcase, test_RDFAnnotation_replaceAnnotation );
   tcase_add_test(tcase, test_RDFAnnotation_replaceAnnotation1 );
   tcase_add_test(tcase, test_RDFAnnotation_replaceAnnotation2 );
+
+
   suite_add_tcase(suite, tcase);
 
   return suite;

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation2.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation2.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotation2.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -66,6 +66,8 @@
   // The following will return a pointer to a new SBMLDocument.
   d2 = readSBML(filename);
   m2 = d2->getModel();
+
+  free(filename);
 }
 
 
@@ -325,9 +327,12 @@
                             RDFAnnotation2_teardown);
 
   tcase_add_test(tcase, test_RDFAnnotation2_getModelHistory );
+  
+  // // memory leaks unresolved
   tcase_add_test(tcase, test_RDFAnnotation2_modelWithHistoryAndCVTerms );
   tcase_add_test(tcase, test_RDFAnnotation2_modelWithHistoryAndMultipleModifiedDates );
   tcase_add_test(tcase, test_RDFAnnotation2_modelWithHistoryWithCharacterReference);
+  
   suite_add_tcase(suite, tcase);
 
   return suite;

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationC.c
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationC.c	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationC.c	2014-09-23 08:51:23 UTC (rev 21152)
@@ -67,6 +67,8 @@
   // The following will return a pointer to a new SBMLDocument.
   d = readSBML(filename);
   m = SBMLDocument_getModel(d);
+
+  free(filename);
 }
 
 
@@ -329,8 +331,11 @@
   tcase_add_test(tcase, test_RDFAnnotation_C_getModelHistory );
   tcase_add_test(tcase, test_RDFAnnotation_C_parseModelHistory );
   tcase_add_test(tcase, test_RDFAnnotation_C_parseCVTerms );
+  tcase_add_test(tcase, test_RDFAnnotation_C_accessWithNULL    );
+
+  // // memory leaks unresolved
   tcase_add_test(tcase, test_RDFAnnotation_C_delete );
-  tcase_add_test(tcase, test_RDFAnnotation_C_accessWithNULL    );
+
   suite_add_tcase(suite, tcase);
 
   return suite;

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -69,6 +69,8 @@
   // The following will return a pointer to a new SBMLDocument.
   d = readSBML(filename);
   m = d->getModel();
+
+  free(filename);
 }
 
 
@@ -263,6 +265,7 @@
                             RDFAnnotationMetaid_setup,
                             RDFAnnotationMetaid_teardown);
 
+  // // memory leaks unresolved
   tcase_add_test(tcase, test_RDFAnnotationMetaid_setAnnotation1 );
   tcase_add_test(tcase, test_RDFAnnotationMetaid_setAnnotation2 );
   tcase_add_test(tcase, test_RDFAnnotationMetaid_setAnnotation3 );

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestRunner.c
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestRunner.c	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestRunner.c	2014-09-23 08:51:23 UTC (rev 21152)
@@ -83,7 +83,7 @@
 setTestDataDirectory (void)
 {
   char *srcdir = getenv("srcdir");
-  int  length  = (srcdir == NULL) ? 0 : strlen(srcdir);
+  size_t  length  = (srcdir == NULL) ? 0 : strlen(srcdir);
 
 
   /**
@@ -133,6 +133,8 @@
 
   srunner_free(runner);
 
+  free(TestDataDirectory);
+
   return num_failed;
 }
 

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestSyncAnnotation.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestSyncAnnotation.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestSyncAnnotation.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -69,6 +69,8 @@
   // The following will return a pointer to a new SBMLDocument.
   d = readSBML(filename);
   m = d->getModel();
+
+  free(filename);
 }
 
 
@@ -141,8 +143,11 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -342,8 +347,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -453,8 +462,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -497,8 +510,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -525,8 +542,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -638,8 +659,12 @@
     "</compartment>";
 
 
-    fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -667,8 +692,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -715,8 +744,12 @@
     "</compartment>";
 
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
   c->unsetModelHistory();
   c->addCVTerm(cv);
   const char * expected1 =
@@ -735,8 +768,12 @@
     "</compartment>";
 
 
-  fail_unless( equals(expected1, c->toSBML()) );
+  sbml = c->toSBML();
 
+  fail_unless( equals(expected1, sbml) );
+
+  free(sbml);
+
   c->setModelHistory(mh);
   c->unsetCVTerms();
   c->addCVTerm(cv);
@@ -777,8 +814,12 @@
     "</compartment>";
 
 
-  fail_unless( equals(expected2, c->toSBML()) );
+  sbml = c->toSBML();
 
+  fail_unless( equals(expected2, sbml) );
+
+  free(sbml);
+
 }
 END_TEST
 
@@ -810,8 +851,11 @@
     "</compartment>";
 
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -862,8 +906,11 @@
     "</compartment>";
 
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -895,8 +942,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
 
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
+
   c->setModelHistory(mh);
   c->addCVTerm(cv);
   c->unsetCVTerms();
@@ -941,8 +992,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected1, c->toSBML()) );
+  sbml = c->toSBML();
 
+  fail_unless( equals(expected1, sbml) );
+
+  free(sbml);
+
   c->unsetModelHistory();
   c->unsetCVTerms();
   c->addCVTerm(cv);
@@ -972,8 +1027,12 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected2, c->toSBML()) );
+  sbml = c->toSBML();
 
+  fail_unless( equals(expected2, sbml) );
+
+  free(sbml);
+
   c->unsetModelHistory();
   c->unsetCVTerms();
   c->addCVTerm(cv);
@@ -1024,7 +1083,11 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected3, c->toSBML()) );
+  sbml = c->toSBML();
+
+  fail_unless( equals(expected3, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -1107,7 +1170,11 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
+
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -1188,7 +1255,11 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
+
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -1269,7 +1340,11 @@
     "  </annotation>\n"
     "</model>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
+
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -1310,7 +1385,11 @@
     "  </annotation>\n"
     "</compartment>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
+
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -1391,7 +1470,11 @@
     "  </annotation>\n"
     "</model>";
 
-  fail_unless( equals(expected, c->toSBML()) );
+  char * sbml = c->toSBML();
+
+  fail_unless( equals(expected, sbml) );
+
+  free(sbml);
 }
 END_TEST
 
@@ -1408,6 +1491,9 @@
 
   tcase_add_test(tcase, test_SyncAnnotation_noChanges_1 );
   tcase_add_test(tcase, test_SyncAnnotation_noChanges_2 );
+ 
+  // // memory leaks unresolved
+
   tcase_add_test(tcase, test_SyncAnnotation_deleteModelOnly );
   tcase_add_test(tcase, test_SyncAnnotation_deleteModelOnly_1 );
   tcase_add_test(tcase, test_SyncAnnotation_deleteCVTerms );

Modified: branches/libsbml-experimental/src/sbml/annotation/test/TestValidation.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/annotation/test/TestValidation.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/annotation/test/TestValidation.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -147,6 +147,8 @@
   fail_unless (mh->hasRequiredAttributes());
   
   delete mh;
+  delete mc;
+  delete date;
 }
 END_TEST
 
@@ -176,6 +178,8 @@
   fail_unless (!(mh->hasRequiredAttributes()));
   
   delete mh;
+  delete mc;
+  delete date;
 }
 END_TEST
 
@@ -204,6 +208,8 @@
   fail_unless (!(mh->hasRequiredAttributes()));
   
   delete mh;
+  delete mc;
+  delete date;
 }
 END_TEST
 

Modified: branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -226,11 +226,13 @@
 	const std::string &prefix,
 	TestPkgNamespaces *groupsns)
 	: SBasePlugin(uri,prefix, groupsns)
+  , mValue()
 {
 }
 
 TestModelPlugin::TestModelPlugin(const TestModelPlugin& orig)
 	: SBasePlugin(orig)
+  , mValue(orig.mValue)
 {
 }
 
@@ -241,6 +243,7 @@
 {
 	if(&orig!=this)
 	{
+    this->mValue = orig.mValue;
 		this->SBasePlugin::operator =(orig);
 	}    
 	return *this;
@@ -252,6 +255,18 @@
 	return new TestModelPlugin(*this);  
 }
 
+const std::string& 
+TestModelPlugin::getValue() const
+{
+  return mValue;
+}
+void 
+TestModelPlugin::setValue(const std::string& value)
+{
+  mValue = value;
+}
+
+
 SBase*
 	TestModelPlugin::createObject(XMLInputStream& stream)
 {

Modified: branches/libsbml-experimental/src/sbml/extension/test/TestPackage.h
===================================================================
--- branches/libsbml-experimental/src/sbml/extension/test/TestPackage.h	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/extension/test/TestPackage.h	2014-09-23 08:51:23 UTC (rev 21152)
@@ -95,23 +95,26 @@
 class TestModelPlugin : public SBasePlugin
 {
 public:
+  TestModelPlugin(const std::string &uri, const std::string &prefix,
+    TestPkgNamespaces *groupsns);
+  TestModelPlugin(const TestModelPlugin& orig);
+  virtual ~TestModelPlugin();
+  TestModelPlugin& operator=(const TestModelPlugin& orig);
+  virtual TestModelPlugin* clone() const;
+  virtual SBase* createObject(XMLInputStream& stream);
+  virtual void writeElements(XMLOutputStream& stream) const;
+  virtual bool hasRequiredElements() const;
 
-	  TestModelPlugin (const std::string &uri, const std::string &prefix,
-                    TestPkgNamespaces *groupsns);
-      TestModelPlugin(const TestModelPlugin& orig);
-	  virtual ~TestModelPlugin ();
-	  TestModelPlugin& operator=(const TestModelPlugin& orig);
-	  virtual TestModelPlugin* clone () const;
-	  virtual SBase* createObject (XMLInputStream& stream);
-	  virtual void writeElements (XMLOutputStream& stream) const;
-	  virtual bool hasRequiredElements() const ;
+  virtual void setSBMLDocument(SBMLDocument* d);
+  virtual void connectToParent(SBase *sbase);
 
-	  virtual void setSBMLDocument (SBMLDocument* d);
-	  virtual void connectToParent (SBase *sbase);
+  virtual void enablePackageInternal(const std::string& pkgURI,
+    const std::string& pkgPrefix, bool flag);
+  const std::string& getValue() const;
+  void setValue(const std::string& value);
 
-	  virtual void enablePackageInternal(const std::string& pkgURI,
-                                     const std::string& pkgPrefix, bool flag);
-
+protected:
+  std::string mValue;
 };
 LIBSBML_CPP_NAMESPACE_END
 #endif //__cplusplus

Modified: branches/libsbml-experimental/src/sbml/extension/test/TestSBMLExtension.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/extension/test/TestSBMLExtension.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/extension/test/TestSBMLExtension.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -136,7 +136,45 @@
 }
 END_TEST
 
+START_TEST(test_SBMLExtension_reenable)
+{  
+  TestPkgNamespaces ns(3, 1, 1);
+  SBMLDocument doc(&ns);
+  Model* model = doc.createModel();  
+  TestModelPlugin* mPlugin = dynamic_cast<TestModelPlugin*>( model->getPlugin("test") );
+  fail_unless(mPlugin != NULL);
+  mPlugin->setValue("foo");
+  fail_unless(mPlugin->getValue() == "foo");
+  fail_unless(doc.getNumDisabledPlugins() == 0);
 
+  // disable plugin 
+  doc.disablePackage(TestExtension::getXmlnsL3V1V1(), "test");
+  fail_unless(doc.getNumDisabledPlugins() == 1);
+  mPlugin = dynamic_cast<TestModelPlugin*>(model->getPlugin("test"));
+  fail_unless(mPlugin == NULL);
+
+  // re-enable plugin
+  doc.enablePackage(TestExtension::getXmlnsL3V1V1(), "test", true);
+  fail_unless(doc.getNumDisabledPlugins() == 0);
+  mPlugin = dynamic_cast<TestModelPlugin*>(model->getPlugin("test"));
+  fail_unless(mPlugin != NULL);
+  fail_unless(mPlugin->getValue() == "foo");
+
+  // disable again
+  doc.disablePackage(TestExtension::getXmlnsL3V1V1(), "test");
+  fail_unless(doc.getNumDisabledPlugins() == 1);
+  doc.deleteDisabledPlugins();
+  fail_unless(doc.getNumDisabledPlugins() == 0);
+
+  // enable plugin
+  doc.enablePackage(TestExtension::getXmlnsL3V1V1(), "test", true);
+  mPlugin = dynamic_cast<TestModelPlugin*>(model->getPlugin("test"));
+  fail_unless(mPlugin != NULL);
+  fail_unless(mPlugin->getValue().empty());
+
+}
+END_TEST
+
 Suite *
 create_suite_SBMLExtension (void)
 {
@@ -145,6 +183,7 @@
 	
   tcase_add_test( tcase, test_SBMLExtension );
   tcase_add_test( tcase, test_SBMLExtension_c_api );
+  tcase_add_test( tcase, test_SBMLExtension_reenable );
   
   suite_add_tcase(suite, tcase);
 

Modified: branches/libsbml-experimental/src/sbml/packages/comp/extension/CompModelPlugin.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/extension/CompModelPlugin.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/packages/comp/extension/CompModelPlugin.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -693,14 +693,17 @@
       return LIBSBML_OPERATION_FAILED;
     }
     
-    // if we have a transformer specified, then we need to propagate it, so it can
-    // be used
-    if (isSetTransformer())
-    {
-      CompModelPlugin* other = dynamic_cast<CompModelPlugin*>(submodinst->getPlugin("comp"));
-      if (other != NULL)
-        other->setTransformer(getTransformer());
-    }
+    //// if we have a transformer specified, then we need to propagate it, so it can
+    //// be used
+
+    // this needs to happen in Submodel:instantiate
+
+    //if (isSetTransformer())
+    //{
+    //  CompModelPlugin* other = dynamic_cast<CompModelPlugin*>(submodinst->getPlugin("comp"));
+    //  if (other != NULL)
+    //    other->setTransformer(getTransformer());
+    //}
   }
 
   // Next, recursively find all the targets of SBaseRef elements 

Modified: branches/libsbml-experimental/src/sbml/packages/comp/extension/CompSBMLDocumentPlugin.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/extension/CompSBMLDocumentPlugin.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/packages/comp/extension/CompSBMLDocumentPlugin.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -950,6 +950,7 @@
     converter->setDocument(&dummyDoc);
     
     int result = converter->convert();
+    delete converter;
 
     if (result == LIBSBML_OPERATION_SUCCESS)
     {

Modified: branches/libsbml-experimental/src/sbml/packages/comp/extension/test/TestExtensionObjects.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/extension/test/TestExtensionObjects.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/packages/comp/extension/test/TestExtensionObjects.cpp	2014-09-23 08:51:23 UTC (rev 21152)
@@ -63,7 +63,7 @@
   fail_unless(doc->isPackageEnabled("comp") == true);
   fail_unless(doc->getModel()->isPackageEnabled("comp") == true);
   fail_unless(doc->getModel()->getCompartment(0)->isPackageEnabled("comp") == true);
-
+  delete doc;
 }
 END_TEST
 
@@ -91,6 +91,7 @@
   fail_unless(submodref->getModelRef()=="ID1");
   fail_unless(mplugin->removeSubmodel(3)==NULL);
   fail_unless(mplugin->removeSubmodel(0)==submod);
+  delete submod;
   fail_unless(mplugin->getSubmodel("submod1")==NULL);
 
   fail_unless(mplugin->getNumPorts()==0);
@@ -111,6 +112,7 @@
   fail_unless(portref->getIdRef()=="ID1");
   fail_unless(mplugin->removePort(3)==NULL);
   fail_unless(mplugin->removePort(0)==port);
+  delete port;
   fail_unless(mplugin->getPort("port1")==NULL);
 }
 END_TEST
@@ -143,6 +145,7 @@
   fail_unless(reref->getDeletion()=="ID1");
   fail_unless(pplugin->removeReplacedElement(3)==NULL);
   fail_unless(pplugin->removeReplacedElement(0)==re);
+  delete re;
   fail_unless(pplugin->getReplacedElement(1)==NULL);
 
   fail_unless(pplugin->isSetReplacedBy()==false);
@@ -185,6 +188,7 @@
   fail_unless(moddefref->getId()=="ID1");
   fail_unless(docplugin->removeModelDefinition(3)==NULL);
   fail_unless(docplugin->removeModelDefinition(0)==moddef);
+  delete moddef;
   fail_unless(docplugin->getModelDefinition("moddef1")==NULL);
 
   fail_unless(docplugin->getNumExternalModelDefinitions()==0);
@@ -205,6 +209,7 @@
   fail_unless(exmoddefref->getModelRef()=="ID1");
   fail_unless(docplugin->removeExternalModelDefinition(3)==NULL);
   fail_unless(docplugin->removeExternalModelDefinition(0)==exmoddef);
+  delete exmoddef;
   fail_unless(docplugin->getExternalModelDefinition("exmoddef1")==NULL);
 
 }

Modified: branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp	2014-09-22 14:37:22 UTC (rev 21151)
+++ branches/libsbml-experimental/src/sbml/packages/comp/sbml/Submodel.cpp	...
 
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